yeah, those weird flying things are seen transporting ultima weapon early in 2.0.

I guess the few that remain fly around patrolling the skies and shooting down whatever airships they can? It was said that the reason why they don't use airships as often anymore is due to the garleans shooting them down.

However, I do remember a scene in 1.0 where the Garleans were bombing Gridania from above. Pretty sure there was quest to shoot them down